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   <TITLE>Completeness check</TITLE>
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<H1><A HREF=".">Aqua server</A></H1>
<H2><A HREF="./compl_chk.html">
Completeness check</A></H2>
<BR><BR>

<HR>

<P>
Please have a look through the documentation of the 
<A HREF="../html/AquaCompl.html">completeness check</A>,
especially the 
<A HREF="../html/compl_method.html">method</A> and 
<A HREF="../html/compl_output.html">output</A> section might interest you.
</P>

<HR><FORM METHOD="POST"
ACTION="CGI_LOC/Aqua/compl_chk.pl" 
ENCTYPE="multipart/form-data">

<P>You need to supply both a restraint and a coordinate file.</P>

<P><B>NOE file:<INPUT 
TYPE="file"
NAME="NOE_FILE" 
VALUE=""
SIZE=50 ></B>

<P>The restraint file should be in the AQUA format described 
<A HREF="http://www.nmr.chem.uu.nl/users/rull/pcheck_dir/nmr_manual/manappb.html">here</A>.
You can use the <A HREF="brsvg.noe">example</A> restraint file (derived
from <A HREF="ftp://pdb.pdb.bnl.gov//nmr_restraints/1brv.mr.Z">PDB mr file
for 1BRV</A>).

<P>
Please use this <A HREF="qconvert.html">conversion server</A>
if you are unable to provide the AQUA formatted restraint file. 
<BR>Only the NOE upper bound distance information will be used in this
check.</P>

<BR><B>PDB file:<INPUT 
TYPE="file" 
NAME="PDB_FILE" 
VALUE="" 
SIZE=50 ></B>

<P>
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-pdb" CHECKED> PDB
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-xplor"> XPLOR
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-molmol"> MOLMOL
</P>

<P>The coordinate file should be in <A HREF="http://www.pdb.bnl.gov/pdb-docs/Format.doc/Contents_Guide_21.html">PDB
format</A>. You can use the <A HREF="brsvg.pdb">example</A> structure (first
2 models of PDB entry <A HREF="http://www.pdb.bnl.gov/pdb-bin/send-pdb?filename=1brv">1BRV</A>
). If you use an XPLOR or MOLMOL type of pdb file you can try selecting that
type.

<P><B>OPTIONS:</B>
<TABLE BORDER CELLSPACING=0 CELLPADDING=10 >
<TR>
<TD>
<DL>
<DT>
Include intra-residual contacts:</DT>

<DD>
<INPUT TYPE="radio" NAME="Intra_residual"
VALUE="true"   CHECKED     >yes
<INPUT TYPE="radio" NAME="Intra_residual"
VALUE="false"              >no</DD>

<DT>
Use set of observable atoms:</DT>

<DD>
<SELECT NAME="Observable_set" SINGLE SIZE=3">
<OPTION VALUE="standard" SELECTED >Standard
<OPTION VALUE="no_stereo"> Standard, no individual prochiral groups
<OPTION VALUE="all_stereo">Standard, all individual prochiral groups
<OPTION VALUE="hnha">Only amides and alpha protons
<OPTION VALUE="hn">Only amides
<OPTION VALUE="theor">All theoretically possible with NMR
<OPTION VALUE="heavy">All non-hydrogens
</SELECT></DD>

<P>NOTE: Please have a look at the different sets of observable atoms 
<A HREF="../html/observables.html">here</A>.</DL>

<DT>
Averaging over models by 
&lt;r<SUP>a</SUP>&gt;<SUP>1/a</SUP>
(-9.0 < a < 9.0):</DT>

<DD>
<INPUT TEXT NAME="Averaging_power" VALUE="1.0" size=3></DD>

<DT> <A HREF="../html/terseness.html">Terseness</A> of the output (0[most verbose] through 9[default]):</DT>
<DD>
<INPUT TEXT NAME="Terseness" VALUE="9" size=2></DD>

</TD>

<TD>
<DL>
<DT>
EXPERIMENTAL SHELLS</DT>

<DT>
Minimum distance:</DT>

<DD>
<INPUT TEXT NAME="Min_distance_rst" VALUE="2.0" size=3></DD>

<DT>
Maximum distance (<= 8 &Aring):</DT>

<DD>
<INPUT TEXT NAME="Max_distance_rst" VALUE="4.0" size=3></DD>

<DT>
Number of shells (<= 20):</DT>

<DD>
<INPUT TEXT NAME="Number_shells_rst" VALUE="4" size=3></DD>
</DL>
</TD>

<TD>
<DL>
<DT>
MODEL-BASED SHELLS</DT>

<DT>
Minimum distance:</DT>

<DD>
<INPUT TEXT NAME="Min_distance_prs" VALUE="2.0" size=3></DD>

<DT>
Maximum distance (<= 8 &Aring):</DT>

<DD>
<INPUT TEXT NAME="Max_distance_prs" VALUE="4.0" size=3></DD>

<DT>
Number of shells (<= 20):</DT>

<DD>
<INPUT TEXT NAME="Number_shells_prs" VALUE="4" size=3></DD>
</DL>
</TD>
</TR>
</TABLE>

<P><INPUT 
TYPE="submit" 
NAME="SUBMIT"
VALUE="Start uploading the Query!"></FORM>
<HR>

<P>Contact the 
<A HREF="mailto:jurgenfd@gmail.com">author</A> or 
<A HREF="mailto:WEBMASTER">webmaster</A>
for help, when required.
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